「view this page in B3 βῆτα server」

Revisions №61171

branch: master 「№61171」
Commited by: Vikram K. Mulligan
GitHub commit link: 「20a7d010d46d9d2e」 「№4544」
Difference from previous tested commit:  code diff
Commit date: 2020-03-07 15:44:33
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug build.cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels build.ninja_debug graphics static build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration.valgrind integration maintenance.documentation performance profile release.PyRosetta4.MinSizeRel release.source scientific.dock_glycans scientific.enzyme_design scientific.loop_modeling_ccd_12res.debug scientific.mp_domain_assembly scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_sequence_recovery.debug scientific.relax_fast_5iter scientific.rna_denovo_favorites scientific.stepwise_rna_favorites.debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release gcc-9.gcc.unit util.apps

Merge pull request #4544 from RosettaCommons/vmullig/peptidestubmover_respect_ACE_and_NME Feature addition for the PeptideStubMover Currently, the `PeptideStubMover` can only append or prepend to naked termini or to the default terminal types. However, it would be convenient to be able to append to a C-methylamidated residue or to prepend on an N-acetylated residue, preserving the mainchain dihedral values when we do so (since these terminal modifications are meant to emulate an amide bond to a preceding or following residue). This pull request adds this ability. This PR also makes a minor change to the `FoldTree` and `Edge` classes (adding a new `Edge` constructor and a new `FoldTree::add_edge()` method for convenience, each of which takes slightly different parameters than the existing methods). I've ensured that these are covered in the `FoldTree` unit tests. Tasks: - [x] Add the feature. - [x] Unit-test it. - [x] Debug it. - [x] Beauty. - [x] Documentation.

...
Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/apps/public/rosetta_scripts/rosetta_scripts.cc src/basic/citation_manager/Citation.cc src/basic/citation_manager/CitationCollection.cc src/basic/citation_manager/CitationManager.cc src/basic/citation_manager/UnpublishedModuleAuthor.cc src/basic/citation_manager/UnpublishedModuleInfo.cc src/core/chemical/carbohydrates/CarbohydrateInfoManager.cc src/core/energy_methods/AACompositionEnergy.cc src/core/energy_methods/NetChargeEnergy.cc src/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/ApproximateBuriedUnsatPenalty.cc src/core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenalty.cc src/core/pack/guidance_scoreterms/hbnet_energy/HBNetEnergy.cc src/core/pack/guidance_scoreterms/voids_penalty_energy/VoidsPenaltyEnergy.cc src/core/pack/palette/CustomBaseTypePackerPalette.cc src/core/pack/palette/DefaultPackerPalette.cc src/core/pack/palette/NCAADefaultPackerPalette.cc src/core/pack/palette/NoDesignPackerPalette.cc src/core/scoring/ScoreFunction.cc src/core/select/residue_selector/AndResidueSelector.cc src/core/select/residue_selector/LayerSelector.cc src/core/select/residue_selector/NeighborhoodResidueSelector.cc src/core/select/residue_selector/NotResidueSelector.cc src/core/select/residue_selector/OrResidueSelector.cc src/core/select/residue_selector/SliceResidueSelector.cc src/core/simple_metrics/metrics/DihedralDistanceMetric.cc src/core/simple_metrics/metrics/InteractionEnergyMetric.cc src/core/simple_metrics/metrics/RMSDMetric.cc src/core/simple_metrics/metrics/ResidueSummaryMetric.cc src/core/simple_metrics/metrics/SasaMetric.cc src/core/simple_metrics/metrics/SecondaryStructureMetric.cc src/core/simple_metrics/metrics/SelectedResidueCountMetric.cc src/core/simple_metrics/metrics/SelectedResiduesMetric.cc src/core/simple_metrics/metrics/SelectedResiduesPyMOLMetric.cc src/core/simple_metrics/metrics/SequenceMetric.cc src/core/simple_metrics/metrics/SequenceSimilarityMetric.cc src/core/simple_metrics/metrics/TimingProfileMetric.cc src/core/simple_metrics/metrics/TotalEnergyMetric.cc src/protocols/analysis/GlycanInfoMover.cc src/protocols/analysis/simple_metrics/RunSimpleMetricsMover.cc src/protocols/antibody/AntibodyCDRGrafter.cc src/protocols/antibody/AntibodyNumberingConverterMover.cc src/protocols/antibody/constraints/CDRDihedralConstraintMover.cc src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.cc src/protocols/antibody/constraints/ParatopeSiteConstraintMover.cc src/protocols/antibody/design/AntibodyDesignMover.cc src/protocols/antibody/design/MutateFrameworkForCluster.cc src/protocols/calc_taskop_movers/CreateSequenceMotifMover.cc src/protocols/carbohydrates/CreateGlycanSequonMover.cc src/protocols/carbohydrates/GlycanSampler.cc src/protocols/carbohydrates/GlycanTreeMinMover.cc src/protocols/carbohydrates/GlycanTreeModeler.cc src/protocols/carbohydrates/IdealizeAnomericHydrogens.cc src/protocols/carbohydrates/LinkageConformerMover.cc src/protocols/carbohydrates/RingPlaneFlipMover.cc src/protocols/carbohydrates/SimpleGlycosylateMover.cc src/protocols/carbohydrates/TautomerizeAnomerMover.cc src/protocols/cyclic_peptide/SymmetricCycpepAlign.cc src/protocols/cyclic_peptide/TryDisulfPermutations.cc src/protocols/denovo_design/movers/FastDesign.cc src/protocols/enzymatic_movers/EnzymaticMover.cc src/protocols/enzymatic_movers/GlycosyltransferaseMover.cc src/protocols/enzymatic_movers/KinaseMover.cc src/protocols/features/ReportToDB.cc src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc src/protocols/grafting/AnchoredGraftMover.cc src/protocols/grafting/CCDEndsGraftMover.cc src/protocols/grafting/simple_movers/DeleteRegionMover.cc src/protocols/grafting/simple_movers/InsertPoseIntoPoseMover.cc src/protocols/grafting/simple_movers/KeepRegionMover.cc src/protocols/grafting/simple_movers/ReplaceRegionMover.cc src/protocols/helical_bundle/BackboneGridSampler.cc src/protocols/helical_bundle/BundleGridSampler.cc src/protocols/helical_bundle/MakeBundle.cc src/protocols/helical_bundle/PerturbBundle.cc src/protocols/indexed_structure_store/filters/FragmentLookupFilter.cc src/protocols/ligand_docking/FinalMinimizer.cc src/protocols/ligand_docking/HighResDocker.cc src/protocols/ligand_docking/HighResEnsemble.cc src/protocols/ligand_docking/InterfaceScoreCalculator.cc src/protocols/ligand_docking/ProtLigEnsemble.cc src/protocols/ligand_docking/StartFrom.cc src/protocols/ligand_docking/Transform.cc src/protocols/ligand_docking/TransformEnsemble.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loop_grower/SheetSampler.cc src/protocols/monte_carlo/GenericMonteCarloMover.cc src/protocols/moves/Mover.cc src/protocols/moves/MoverContainer.cc src/protocols/protein_interface_design/movers/LoopOver.cc src/protocols/relax/FastRelax.cc src/protocols/relax/RelaxProtocolBase.cc src/protocols/rosetta_scripts/ParsedProtocol.cc src/protocols/simple_moves/BBDihedralSamplerMover.cc src/protocols/simple_moves/ConvertRealToVirtualMover.cc src/protocols/simple_moves/ConvertVirtualToRealMover.cc src/protocols/simple_moves/DeleteChainsMover.cc src/protocols/simple_moves/RingConformationMover.cc src/protocols/simple_moves/SetupMetalsMover.cc src/protocols/simple_moves/SimpleThreadingMover.cc
Test: linux.clang.scientific.dock_glycans

 View log

Loading...

 View log in dialog  View log in log in separate window